Starting phenix.real_space_refine
on Tue Feb  3 12:38:36 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9p1t_71131/02_2026/9p1t_71131.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p1t_71131/02_2026/9p1t_71131.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p1t_71131/02_2026/9p1t_71131.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p1t_71131/02_2026/9p1t_71131.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p1t_71131/02_2026/9p1t_71131.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p1t_71131/02_2026/9p1t_71131.cif"
  }
  resolution = 3.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    1456      2.51       5
     N     348      2.21       5
     O     357      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2179
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 271, 2090
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 9, 'TRANS': 261}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 10
      Conformer: "B"
        Number of residues, atoms: 271, 2090
          Classifications: {'peptide': 271}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 9, 'TRANS': 261}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 10
          bond proxies already assigned to first conformer: 2135
    Chain: "A"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 83
          Unusual residues: {'LMN': 1, 'ZMA': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 5
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ASER A  35 " occ=0.60
      ... (10 atoms not shown)
      pdb=" OG BSER A  35 " occ=0.40
  Time building chain proxies: 1.02, per 1000 atoms: 0.47
  Number of scatterers: 2179
  At special positions: 0
  Unit cell: (50.096, 71.104, 63.024, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O     357      8.00
     N     348      7.00
     C    1456      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  74 " - pdb=" SG  CYS A 146 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  77 " - pdb=" SG  CYS A 166 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.18
  Conformation dependent library (CDL) restraints added in 93.2 milliseconds
  

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  520

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 1 sheets defined
      89.3% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 34
    Processing helix  chain 'A' and resid 40 through 58
      removed outlier: 3.822A  pdb=" N   PHE A  44 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 69
    Processing helix  chain 'A' and resid 73 through 108
      removed outlier: 5.251A  pdb=" N   VAL A  84 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   LEU A  85 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL A  86 " --> pdb=" O   CYS A  82 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 116
    Processing helix  chain 'A' and resid 117 through 137
    Processing helix  chain 'A' and resid 137 through 142
      removed outlier: 3.698A  pdb=" N   LEU A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 172
    Processing helix  chain 'A' and resid 173 through 179
    Processing helix  chain 'A' and resid 186 through 208
      removed outlier: 3.520A  pdb=" N   LEU A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 355
      removed outlier: 3.530A  pdb=" N   ILE A 334 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA A 335 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
      removed outlier: 3.504A  pdb=" N   CYS A 355 " --> pdb=" O   PHE A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 388
      removed outlier: 3.671A  pdb=" N   ASN A 376 " --> pdb=" O   LEU A 372 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   SER A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   VAL A 378 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL A 379 " --> pdb=" O   THR A 375 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ASN A 380 " --> pdb=" O   ASN A 376 " (cutoff:3.500A)
      Proline residue:  A 381  - end of helix
    Processing helix  chain 'A' and resid 388 through 399
    Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72

    171 hydrogen bonds defined for protein.
    510 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.43

  Time building geometry restraints manager: 0.23 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 558
        1.34 -     1.45: 423
        1.45 -     1.57: 1233
        1.57 -     1.69: 0
        1.69 -     1.81: 23
  Bond restraints: 2237
  Sorted by residual:
  bond pdb=" N   ILE A 108 "
       pdb=" CA  ILE A 108 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.23e-02 6.61e+03 7.56e+00
  bond pdb=" N   ILE A  53 "
       pdb=" CA  ILE A  53 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.31e+00
  bond pdb=" N   VAL A  55 "
       pdb=" CA  VAL A  55 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.031 1.17e-02 7.31e+03 7.24e+00
  bond pdb=" N   ILE A 106 "
       pdb=" CA  ILE A 106 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.036 1.42e-02 4.96e+03 6.29e+00
  bond pdb=" N   HIS A 374 "
       pdb=" CA  HIS A 374 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.33e-02 5.65e+03 5.18e+00
  ... (remaining 2232 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 2949
        1.94 -     3.87: 89
        3.87 -     5.81: 18
        5.81 -     7.74: 1
        7.74 -     9.68: 1
  Bond angle restraints: 3058
  Sorted by residual:
  angle pdb=" CB  MET A 193 "
        pdb=" CG  MET A 193 "
        pdb=" SD  MET A 193 "
      ideal   model   delta    sigma   weight residual
     112.70  103.02    9.68 3.00e+00 1.11e-01 1.04e+01
  angle pdb=" N   VAL A  55 "
        pdb=" CA  VAL A  55 "
        pdb=" C   VAL A  55 "
      ideal   model   delta    sigma   weight residual
     110.62  106.95    3.67 1.14e+00 7.69e-01 1.03e+01
  angle pdb=" CA  ASN A 380 "
        pdb=" C   ASN A 380 "
        pdb=" N   PRO A 381 "
      ideal   model   delta    sigma   weight residual
     118.44  122.89   -4.45 1.59e+00 3.96e-01 7.82e+00
  angle pdb=" CA  TRP A 143 "
        pdb=" CB  TRP A 143 "
        pdb=" CG  TRP A 143 "
      ideal   model   delta    sigma   weight residual
     113.60  118.86   -5.26 1.90e+00 2.77e-01 7.66e+00
  angle pdb=" CA  ILE A  53 "
        pdb=" C   ILE A  53 "
        pdb=" O   ILE A  53 "
      ideal   model   delta    sigma   weight residual
     121.17  118.29    2.88 1.06e+00 8.90e-01 7.40e+00
  ... (remaining 3053 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 1234
       17.15 -    34.29: 91
       34.29 -    51.44: 13
       51.44 -    68.59: 5
       68.59 -    85.74: 4
  Dihedral angle restraints: 1347
    sinusoidal: 547
      harmonic: 800
  Sorted by residual:
  dihedral pdb=" CB  CYS A  77 "
           pdb=" SG  CYS A  77 "
           pdb=" SG  CYS A 166 "
           pdb=" CB  CYS A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.74   85.74     1      1.00e+01 1.00e-02 8.89e+01
  dihedral pdb=" CB  CYS A  74 "
           pdb=" SG  CYS A  74 "
           pdb=" SG  CYS A 146 "
           pdb=" CB  CYS A 146 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  174.68  -81.68     1      1.00e+01 1.00e-02 8.21e+01
  dihedral pdb=" CA  PHE A 182 "
           pdb=" C   PHE A 182 "
           pdb=" N   PHE A 183 "
           pdb=" CA  PHE A 183 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.44  -16.56     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 1344 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 303
       0.057 -    0.113: 60
       0.113 -    0.170: 8
       0.170 -    0.226: 4
       0.226 -    0.283: 1
  Chirality restraints: 376
  Sorted by residual:
  chirality pdb=" CA  ASN A 380 "
            pdb=" N   ASN A 380 "
            pdb=" C   ASN A 380 "
            pdb=" CB  ASN A 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CA  ILE A 108 "
            pdb=" N   ILE A 108 "
            pdb=" C   ILE A 108 "
            pdb=" CB  ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  LEU A 343 "
            pdb=" N   LEU A 343 "
            pdb=" C   LEU A 343 "
            pdb=" CB  LEU A 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 373 not shown)

  Planarity restraints: 357
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 179 "    0.014 2.00e-02 2.50e+03   2.74e-02 7.53e+00
        pdb=" C   TYR A 179 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   TYR A 179 "    0.018 2.00e-02 2.50e+03
        pdb=" N   PHE A 180 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 182 "    0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" C   PHE A 182 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   PHE A 182 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE A 183 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  60 "    0.025 5.00e-02 4.00e+02   3.79e-02 2.30e+00
        pdb=" N   PRO A  61 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A  61 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  61 "    0.022 5.00e-02 4.00e+02
  ... (remaining 354 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 469
        2.78 -     3.31: 2248
        3.31 -     3.84: 3687
        3.84 -     4.37: 4310
        4.37 -     4.90: 7293
  Nonbonded interactions: 18007
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  41 "
            pdb=" OD2 ASP A 101 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" NH1 ARG A 205 "
            pdb=" OAL LMN A 501 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" OD1 ASN A 175 "
            pdb=" N   TYR A 176 "
     model   vdw
     2.408 3.120
  nonbonded pdb=" O   LEU A  37 "
            pdb=" ND2 ASN A  42 "
     model   vdw
     2.419 3.120
  nonbonded pdb=" NE1 TRP A 143 "
            pdb=" OD1 ASN A 175 "
     model   vdw
     2.476 3.120
  ... (remaining 18002 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.40 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.710
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   2239  Z= 0.317
  Angle     :  0.766   9.676   3062  Z= 0.433
  Chirality :  0.051   0.283    376
  Planarity :  0.005   0.038    357
  Dihedral  : 12.896  83.866    821
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  0.45 %
    Favored  : 98.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.50), residues: 268
  helix:  1.69 (0.35), residues: 222
  sheet:  None (None), residues: 0
  loop : -0.49 (0.77), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 205 
 TYR   0.005   0.001   TYR A 179 
 PHE   0.009   0.001   PHE A 182 
 TRP   0.016   0.002   TRP A 143 
 HIS   0.000   0.000   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 ( 2237)
  covalent geometry    : angle       0.76535 ( 3058)
  SS BOND              : bond        0.00160 (    2)
  SS BOND              : angle       1.32575 (    4)
  hydrogen bonds       : bond        0.13328 (  171)
  hydrogen bonds       : angle       5.20345 (  510)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 13
  time to evaluate  : 0.043 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 15
  average time/residue: 0.0234
  time to fit residues: 0.5108
Evaluate side-chains
  12 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 10
  time to evaluate  : 0.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  143 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0770
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.5940

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
A 181 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.168537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.131561 restraints weight = 4736.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 3.59
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3545
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3545
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.0898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2239  Z= 0.136
  Angle     :  0.599   7.562   3062  Z= 0.307
  Chirality :  0.042   0.269    376
  Planarity :  0.005   0.039    357
  Dihedral  : 10.752  84.281    397
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.00 %
    Favored  : 94.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.70 (0.49), residues: 268
  helix:  2.23 (0.34), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.62 (0.65), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 205 
 TYR   0.008   0.001   TYR A 112 
 PHE   0.011   0.001   PHE A 180 
 TRP   0.009   0.001   TRP A 342 
 HIS   0.002   0.001   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 2237)
  covalent geometry    : angle       0.59757 ( 3058)
  SS BOND              : bond        0.00259 (    2)
  SS BOND              : angle       1.10580 (    4)
  hydrogen bonds       : bond        0.03579 (  171)
  hydrogen bonds       : angle       3.63778 (  510)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 13
  time to evaluate  : 0.042 
Fit side-chains
REVERT: A  330 SER cc_start: 0.8653 (t) cc_final: 0.8028 (m)
  outliers start: 1
  outliers final: 1
  residues processed: 14
  average time/residue: 0.0407
  time to fit residues: 0.7188
Evaluate side-chains
  13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 12
  time to evaluate  : 0.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 22 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.167080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.128049 restraints weight = 6537.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 5.01
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3735
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3735 r_free = 0.3735    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2239  Z= 0.136
  Angle     :  0.576   7.530   3062  Z= 0.294
  Chirality :  0.042   0.252    376
  Planarity :  0.005   0.046    357
  Dihedral  : 10.740  88.198    395
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.49), residues: 268
  helix:  2.28 (0.34), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.60 (0.65), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 205 
 TYR   0.007   0.001   TYR A 112 
 PHE   0.009   0.001   PHE A 180 
 TRP   0.007   0.001   TRP A  29 
 HIS   0.001   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 2237)
  covalent geometry    : angle       0.57550 ( 3058)
  SS BOND              : bond        0.00209 (    2)
  SS BOND              : angle       0.90493 (    4)
  hydrogen bonds       : bond        0.03399 (  171)
  hydrogen bonds       : angle       3.49600 (  510)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.042 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0204
  time to fit residues: 0.3794
Evaluate side-chains
  11 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.165421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.126245 restraints weight = 6077.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 4.70
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3592 r_free = 0.3592    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   2239  Z= 0.147
  Angle     :  0.596   7.437   3062  Z= 0.301
  Chirality :  0.042   0.241    376
  Planarity :  0.005   0.042    357
  Dihedral  : 10.578  88.146    393
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  7.27 %
    Favored  : 92.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.66 (0.49), residues: 268
  helix:  2.20 (0.34), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.60 (0.67), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 205 
 TYR   0.020   0.002   TYR A 176 
 PHE   0.012   0.001   PHE A 180 
 TRP   0.007   0.001   TRP A  29 
 HIS   0.001   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 2237)
  covalent geometry    : angle       0.59520 ( 3058)
  SS BOND              : bond        0.00199 (    2)
  SS BOND              : angle       0.87980 (    4)
  hydrogen bonds       : bond        0.03437 (  171)
  hydrogen bonds       : angle       3.48888 (  510)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 15
  time to evaluate  : 0.042 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0371
  time to fit residues: 0.7625
Evaluate side-chains
  11 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.193817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.154457 restraints weight = 4897.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 3.94
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3897 r_free = 0.3897    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3897 r_free = 0.3897    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2239  Z= 0.140
  Angle     :  0.597   7.417   3062  Z= 0.301
  Chirality :  0.041   0.227    376
  Planarity :  0.005   0.049    357
  Dihedral  : 10.428  86.431    393
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  9.09 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.69 (0.49), residues: 268
  helix:  2.21 (0.34), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.58 (0.68), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 205 
 TYR   0.014   0.002   TYR A 176 
 PHE   0.010   0.001   PHE A 180 
 TRP   0.006   0.001   TRP A  29 
 HIS   0.001   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 2237)
  covalent geometry    : angle       0.59584 ( 3058)
  SS BOND              : bond        0.00097 (    2)
  SS BOND              : angle       1.19923 (    4)
  hydrogen bonds       : bond        0.03314 (  171)
  hydrogen bonds       : angle       3.48230 (  510)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.042 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0337
  time to fit residues: 0.7733
Evaluate side-chains
  16 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 21 optimal weight:    0.0060
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.5396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.195143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.161661 restraints weight = 7779.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 4.04
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3966
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2239  Z= 0.122
  Angle     :  0.570   7.307   3062  Z= 0.289
  Chirality :  0.040   0.219    376
  Planarity :  0.005   0.044    357
  Dihedral  : 10.065  84.130    393
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 10.91 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.87 (0.49), residues: 268
  helix:  2.33 (0.34), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.51 (0.70), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 205 
 TYR   0.012   0.001   TYR A 176 
 PHE   0.008   0.001   PHE A 201 
 TRP   0.006   0.001   TRP A  29 
 HIS   0.002   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 2237)
  covalent geometry    : angle       0.56934 ( 3058)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       1.12009 (    4)
  hydrogen bonds       : bond        0.03084 (  171)
  hydrogen bonds       : angle       3.43886 (  510)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 12
  time to evaluate  : 0.040 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 13
  average time/residue: 0.0205
  time to fit residues: 0.4079
Evaluate side-chains
  12 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 11
  time to evaluate  : 0.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 1 optimal weight:    0.1980
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 0 optimal weight:    0.8980
   chunk 10 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0570
   overall best weight:    0.3698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.197027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.158097 restraints weight = 6472.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 4.51
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3945 r_free = 0.3945    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3945 r_free = 0.3945    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   2239  Z= 0.106
  Angle     :  0.538   7.241   3062  Z= 0.274
  Chirality :  0.039   0.214    376
  Planarity :  0.005   0.039    357
  Dihedral  :  9.521  80.167    393
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 10.91 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.12 (0.50), residues: 268
  helix:  2.50 (0.34), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.38 (0.75), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 205 
 TYR   0.011   0.001   TYR A 176 
 PHE   0.006   0.001   PHE A 201 
 TRP   0.006   0.001   TRP A  29 
 HIS   0.001   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 2237)
  covalent geometry    : angle       0.53731 ( 3058)
  SS BOND              : bond        0.00146 (    2)
  SS BOND              : angle       1.06400 (    4)
  hydrogen bonds       : bond        0.02774 (  171)
  hydrogen bonds       : angle       3.38039 (  510)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 11
  time to evaluate  : 0.044 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 13
  average time/residue: 0.0207
  time to fit residues: 0.4135
Evaluate side-chains
  13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 11
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   86 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0770
   chunk 21 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.5738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.195101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.156221 restraints weight = 6591.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 4.67
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3914 r_free = 0.3914    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3914 r_free = 0.3914    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2239  Z= 0.125
  Angle     :  0.565   7.204   3062  Z= 0.286
  Chirality :  0.040   0.212    376
  Planarity :  0.005   0.041    357
  Dihedral  :  9.653  80.000    393
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 12.27 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.03 (0.50), residues: 268
  helix:  2.44 (0.34), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.40 (0.79), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 205 
 TYR   0.010   0.001   TYR A 176 
 PHE   0.008   0.001   PHE A 201 
 TRP   0.005   0.001   TRP A  29 
 HIS   0.002   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 2237)
  covalent geometry    : angle       0.56426 ( 3058)
  SS BOND              : bond        0.00128 (    2)
  SS BOND              : angle       1.03278 (    4)
  hydrogen bonds       : bond        0.03025 (  171)
  hydrogen bonds       : angle       3.40244 (  510)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 11
  time to evaluate  : 0.072 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 13
  average time/residue: 0.0331
  time to fit residues: 0.6664
Evaluate side-chains
  13 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 11
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   86 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 0 optimal weight:    6.9990
   chunk 19 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0370
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.5858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.194936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.157217 restraints weight = 6360.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 4.21
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3923 r_free = 0.3923    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3923 r_free = 0.3923    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2239  Z= 0.125
  Angle     :  0.565   7.175   3062  Z= 0.287
  Chirality :  0.040   0.209    376
  Planarity :  0.005   0.041    357
  Dihedral  :  9.728  80.022    393
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 12.27 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.02 (0.50), residues: 268
  helix:  2.43 (0.34), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.40 (0.80), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 205 
 TYR   0.009   0.001   TYR A 176 
 PHE   0.008   0.001   PHE A 201 
 TRP   0.005   0.001   TRP A  29 
 HIS   0.002   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 2237)
  covalent geometry    : angle       0.56436 ( 3058)
  SS BOND              : bond        0.00150 (    2)
  SS BOND              : angle       1.03875 (    4)
  hydrogen bonds       : bond        0.03042 (  171)
  hydrogen bonds       : angle       3.41669 (  510)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.043 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 14
  average time/residue: 0.0387
  time to fit residues: 0.6899
Evaluate side-chains
  14 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   86 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.193920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.155892 restraints weight = 6057.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3909 rms_B_bonded: 4.13
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3909 r_free = 0.3909    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3909 r_free = 0.3909    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2239  Z= 0.138
  Angle     :  0.587   7.178   3062  Z= 0.297
  Chirality :  0.040   0.212    376
  Planarity :  0.006   0.048    357
  Dihedral  :  9.907  80.628    393
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 12.27 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.95 (0.51), residues: 268
  helix:  2.38 (0.34), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.41 (0.82), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 205 
 TYR   0.009   0.001   TYR A 176 
 PHE   0.009   0.001   PHE A 201 
 TRP   0.005   0.001   TRP A  29 
 HIS   0.001   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 2237)
  covalent geometry    : angle       0.58615 ( 3058)
  SS BOND              : bond        0.00158 (    2)
  SS BOND              : angle       1.04104 (    4)
  hydrogen bonds       : bond        0.03213 (  171)
  hydrogen bonds       : angle       3.44838 (  510)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  536 Ramachandran restraints generated.
    268 Oldfield, 0 Emsley, 268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.067 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 16
  average time/residue: 0.0289
  time to fit residues: 0.7034
Evaluate side-chains
  16 residues out of total 221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   86 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0170
   chunk 11 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0270
   chunk 0 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4076

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.197862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.157585 restraints weight = 6528.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 5.04
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3916 r_free = 0.3916    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3916 r_free = 0.3916    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2239  Z= 0.109
  Angle     :  0.540   7.133   3062  Z= 0.276
  Chirality :  0.039   0.208    376
  Planarity :  0.006   0.047    357
  Dihedral  :  9.537  78.922    393
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 12.73 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.13 (0.50), residues: 268
  helix:  2.50 (0.34), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.33 (0.82), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 205 
 TYR   0.017   0.001   TYR A 176 
 PHE   0.006   0.001   PHE A 201 
 TRP   0.005   0.001   TRP A  29 
 HIS   0.002   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 2237)
  covalent geometry    : angle       0.53943 ( 3058)
  SS BOND              : bond        0.00161 (    2)
  SS BOND              : angle       1.01807 (    4)
  hydrogen bonds       : bond        0.02829 (  171)
  hydrogen bonds       : angle       3.39511 (  510)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 501.84 seconds
wall clock time: 9 minutes 14.87 seconds (554.87 seconds total)